Analysis of genetic diversity in farmers’ rice varieties in Sierra Leone using morphological and AFLP® markers

The objective of the current research was to investigate the status of rice genetic resources in post-war Sierra Leone using both morphological and amplified fragment length polymorphism (AFLP) data. Specifically, we aimed at investigating farmers’ rice genetic resources for homogeneity and differentiation, and at examining the genetic identity of similarly named varieties, including varieties within Sierra Leone, and between Sierra Leone and Guinea. This research was also motivated by the assumption that genetic erosion might have occurred as a result of the civil war. To determine the level of diversity and genetic relationships among farmers’ varieties of rice recently collected in Sierra Leone, two methods were used using subsets of the collected samples: (1) Using morphological data, 74 samples of 29 different varieties were analysed to investigate the relationship between (a) varieties grown in two districts in Sierra Leone, and (b) the two main cultivated species, Oryza sativa and Oryza glaberrima. A dendrogram largely clustered the varieties according to region and to the species to which the varieties belonged. (2) Using AFLP data, three separate investigations were conducted: (a) 33 samples of 10 varieties were investigated to evaluate diversity within and between varieties. The results indicated that the rice varieties possess different levels of intra-variety variation, whereas inter-variety diversity was high enough to distinguish one variety from the other. In particular, an AMOVA analysis revealed that 38 % of the total variation occurred within varieties, and 62 % between varieties. (b) 37 samples of 18 different varieties were investigated to determine the consistency of naming of varieties by farmers. The results showed that there was consistency in the naming by farmers of traditional varieties, but inconsistency in the naming of newly acquired varieties and cultivars. (c) 12 samples were investigated to check the identity of varieties carrying identical names collected in two separate regions, Sierra Leone and the neighbouring country of Guinea. The results indicated no close genetic relationships between the varieties found in Sierra Leone and Guinea despite similarities in the names given to these varieties by farmers, indicating the influence of different cultivation practices in the two countries.     

Comparative analysis of genetic diversity using molecular and morphometric markers in Andrographis paniculata (Burm. f.) Nees

Andrographis paniculata is a medicinal plant of immense therapeutic value. The present study was aimed to elucidate its genetic diversity based on morphochemical and RAPD markers from 53 accessions belonging to 5 eco-geographic regions. Analysis of variance and D ² statistics revealed significant differences in all the metric traits and sufficient inter-cluster distances indicating considerable diversity among the accessions. The complementary approach of RAPD was used to evaluate the genetic dissimilarities among all the accessions using 6 highly polymorphic primers. The average proportion of polymorphic loci across primers was 96.28%. The molecular genetic diversity based on Shannon index per primer averaged 5.585 with values ranging from 3.08 to 8.70 indicating towards wide genetic base. RAPD based UPGMA and D ² cluster analysis also revealed that various accessions available in different eco-geographic regions might have originated from native places of wild abundance. Similarity matrices were generated for molecular markers and morphometric data to determine the degree of congruence between the two. A highly significant but low correlation (r = 0.547, P < 0.001) was obtained thus implying the correspondence between the two. The species is hermaphroditic and a habitual inbreeder. The present study yielded a typical triangular congruence between its breeding system, morphometric traits and RAPD markers thus elucidating the usefulness of complementary approaches to make diversity analysis more explanatory and purposeful for optimum genetic amelioration and effective conservation of its genotypic variability.     

Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center

Lima bean (Phaseolus lunatus L.) is an important crop in traditional Mayan agriculture of the Yucatan Peninsula, Mexico, its Mesoamerican center of diversity. Genetic erosion in this species is currently a threat in this region out of 3 of 21 landraces dominate 71.24% of the cultivated area, and 12 are rare landraces grown only in 6.29%. Using 90 ISSR loci, we estimated the diversity and genetic relationships for 21 landraces to analyzing their risk of genetic erosion, and generate data for their in situ conservation. Total genetic diversity was high (h = 0.29), however it was lower than wild gene pool reported (h = 0.69). The abundant landraces had genetic diversity values lower (h = 0.13, I = 0.17) than the common (h = 0.26, I = 0.33) and rare landraces (h = 0.24, I = 0.27). However, the rare landraces are in a higher risk of genetic erosion due to local extinction. The cluster analysis showed no groups corresponding to morpho-phenological characteristics, geographic origin or traditional classification, which resulted from high inter-landraces gene flow levels. The molecular data confirmed that the domesticated Lima bean pool of the Yucatan Peninsula has a high risk of genetic erosion. If current tendencies in landrace cultivation continue, many will no longer be planted within two to three generations, with a consequent loss of their alleles. Programs urgently need to be established for in situ conservation of Lima bean landraces in this region.     

High genetic diversity revealed in barley (Hordeum vulgare) collected from small-scale farmer’s fields in Eritrea

Remarkable morphological variation has been found within small Eritrean barley fields. Barley was collected from fields approximately 50 m² in size. Spike shape, type, and colour were observed to vary both between and within fields. A set of 39 Simple Sequence Repeats (SSR) markers were used to explore the genetic diversity of the Eritrean barley collected from small-scale farmer’s fields. Significant genetic diversity was found within the barley fields. Out of 240 spikes collected from 24 fields (10 spikes per field), only two spikes from geographically distant fields were genetically similar. Based on the SSR data, individual farmers’ fields were found to possess 97.3% of the genetic variation present in the Eritrean barley. We discuss a strategy to improve the barley yield in Eritrea, and to facilitate the in situ conservation of barley genetic diversity. Gunter Backes and Jihad Orabi contributed equally to this work.     

Public concern about bats (Chiroptera) in Britain: An analysis of enquiries in 1982–1983

The Wildlife and Countryside Act 1981 protected all species of bat and required that, in certain circumstances, advice be sought about them. Analysis of these enquiries produced data about their geographic distribution, the types of problem that arose, the acceptability of the advice provided, the species of bat involved and the organisations receiving the enquiries. The great majority of enquiries related to dwelling-houses and, of these, most resulted from the discovery of bats roosting in the roof.The conservation organisations, mainly the Nature Conservancy Council, proved very successful in persuading householders to leave bats undisturbed; almost all colonies were permitted to remain temporarily and many were permitted to return in succeeding years. Repairs or remedial timber treatment to roofs used by bats were also important sources of enquiries and detailed advice was provided. Most enquiries came from southern England, with a sustained decline towards the north. Pipistrelles were the most common species, followed by long-eared bats. The other 13 species appeared to be involved in relatively few cases.     

Do genetic diversity patterns of soil ammonia-oxidizing microorganisms (AOM) match the habitat types of the NATURA2000 scheme?

Journal of Soils and Sediments - Despite the important role of soil ammonia-oxidizing microorganisms (AOM) in the biogeochemical cycle of nitrogen, a unified view of the factors driving their...     

Development and use of microsatellite markers for genetic diversity analysis of cañahua (<Emphasis Type="Italic">Chenopodium pallidicaule</Emphasis> Aellen)

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritional value (high in protein and mineral content) and ability to thrive in harsh climates make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (Chenopodium quinoa Willd. and Chenopodium petiolare Kunth) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic cañahua sequences produced by 454 pyrosequencing of cañahua genomic DNA. Another 424 microsatellite markers from C. quinoa were also evaluated for cross-species amplification and polymorphism in cañahua. A total of 34 polymorphic microsatellite marker loci were identified which detected a total of 154 alleles with an average of 4.5 alleles per marker locus and an average heterozygosity value of 0.49. A cluster analysis, based on Nei genetic distance, clearly separated from wild cañahua genotypes from the cultivated genotypes. Within the cultivated genotypes, subclades were partitioned by AMOVA analysis into six model-based clusters, including a subclade consisting sole of erect morphotypes. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.     

Long-term effects of fertilization and manuring on productivity and soil biological properties under rice (Oryza sativa)–wheat (Triticum aestivum) sequence in Mollisols

Long-term effects of chemical fertilizers and farmyard manure (FYM) in rice (Oryza sativa)–wheat (Triticum aestivum) cropping system were monitored for two consecutive years after 38 and 39 years on productivity and soil biological properties of Mollisols. The study encompasses varying chemical fertilizer levels of optimum fertilizer rate (120, 26 and 37 kg ha^?1 N, P and K, respectively) for both the crops. The treatments were application of 50% NPK, 100% NPK, 150% NPK, 100% NPK + hand weeding (HW), 100% NPK + Zn, 100% NP, 100% N, 100% NPK + 15 t FYM ha^?1, 100% NPK(-S) and unfertilized control. The rice and wheat yields were highest with 100% NPK + 15 t FYM ha^?1. This treatment also gave maximum and significantly more counts of bacteria, fungi and actinomycetes in soil than all the other treatments after crop harvest. The soil microbial biomass C (410.0 and 407.5 µg g^?1) and N (44.53 and 48.30 µg g^?1) after rice and wheat, respectively, were highest with 100% NPK + 15 t FYM ha^?1, which were significantly higher over all the other treatments. The activities of soil enzymes like dehydrogenase, acid and alkaline phosphatase, arylsulphatase and urease and CO₂ evolution rate with 100% NPK + 15 t FYM ha^?1 were also found significantly higher over the other treatments. Fertilizer treatments with 100% NPK and 150% NPK were comparable and significantly better than application of 50% NPK, 100% N, 100% NP and 100% NPK(-S) in various studied soil biological properties. Integrated use of 100% NPK with FYM sustained the higher yields and soil biological properties under rice–wheat cropping system in Mollisols. Application of Zn and hand weeding with 100% NPK were found better over 100% NPK alone in rice and wheat productivity. Imbalanced use of chemical fertilizers had the harmful effect on soil biological health.     

Mirza (Hacızade) Gökgöl (1897–1981): the great explorer of wheat genetic resources in Turkey

Mirza (Hac?zade) Gökgöl (1897–1981) was a leading agro-ecological plant scientist, agronomist and breeder in Turkey. Gökgöl carried out extensive breeding programmes extensively selecting from local plant genetic resources from across Turkey from 1925 till the 1950s. He collected and evaluated cultivars, landraces and wild relatives, predominantly of wheat, but also of barley, lentil and other crops in Turkey during 1929–1955. He published books on wheat and other cereals, potatoes, castor bean, sweet clover, poppy, and other crops. He was a hardworking pioneer utilizing wheat genetic resources for crop improvement. Since his ample work has hardly been accessible by the English-speaking scientific community today, we are providing an overview of his major work, mainly on wheat. The books he published can still be found in libraries, although with difficulties. However, his articles, leaflets etc., are hardly accessible. Some of them are: Turkish Wheats, vols. 1 and 2, Plant Breeding through Scientific Methods (1928, translation of a book by E. Baur), The Basics of Wheat Breeding (1954), and Agriculture and Breeding of Cool Season Cereals–Wheat, Rye, Barley, and Oats (1969). In addition to the summary of his books, we reviewed his views and discussions about the centres of origin and diversity, and compared with those of Vavilov.     

Effect of nutrient management and straw mulching on crop yield,uptake and soil fertility in rapeseed (Brassica campestris)–greengram (Vigna radiata)–rice (Oryza sativa) cropping system under Gangetic plains of India

An experiment was conducted at Bidhan Chandra Krishi Viswavidyalaya, West Bengal, India during 2001–2003 to study the effect of levels of fertility and straw mulch on a rapeseed (Brassica campestris var yellow sarson)–greengram (Vigna radiata)–rice (Oryza sativa) cropping system under a rainfed upland ecosystem. The experiment was laid out in a split-plot design having 14 treatment combinations of organic and inorganic nutrients along with straw mulch in three replicates. The results revealed that conjunctive use of organic and inorganic nutrients as well as paddy straw mulch resulted higher yield in both rapeseed and greengram, and the residual effects of different levels of fertilization and mulching also gave rise to higher grain yield in the succeeding rice crop. The uptake of nutrients, by the cropping system as a whole, to the tune of 204.29 and 183.00 kg ha^?1 of N, 72.84 and 74.07 kg ha^?1 of P and 179.95 and 175.41 kg ha^?1 of K took place, with the treatment receiving 10 t ha^?1 of farmyard manure (FYM) applied (to rapeseed) along with 50% recommended dose (RD) of NPK to all the crops in the sequence in two consecutive years, respectively. The same treatment resulted in a higher percentage of porosity vis-à-vis lower bulk density. Soil physico-chemical properties were superior in mulch-treated plots compared with no mulch treatment. Application of organic and inorganic nutrients along with proper moisture conservation practices can enhance the yields maintaining a good soil health.     

Potential of AFM–nanothermal analysis to study the microscale thermal characteristics in soils and natural organic matter (NOM)

Purpose  

This exploratory study evaluates the potential of nanothermal analysis (nTA) coupled with atomic force microscopy (AFM) of soil samples for understanding physicochemical processes in soil and for linking the nanospatial and microspatial distribution of thermal characteristics with the macroscopic properties of soil samples.     

Changes in the organic carbon pool of abandoned soils in Russia (1990–2004)

The assessment of the changes in the organic carbon pool in the soils of the Russian Federation that occurred in 1990–2004 was carried out using approximation, soil-geoinformation, and simulation approaches. As a result of the changes in the system of land use, after 1990, the organic carbon storages in the 0- to 20-cm-thick soil layer could be 196–319 Mt depending on the methodology of the calculation applied and taking into account the abandoned area of 14.8 million ha. As compared to the beginning of the 1990s, the organic matter stock in the former plow layer increased by 1.6–5.8%. The great scatter of the data is mainly related to the incertainty of the estimates of the area of arable soils not used any more in agriculture.     

Irrigation of steppe soils in the south of Russia: Problems and solutions (Analysis of Irrigation Practices in 1950–1990)

Experience in irrigation of chernozems in the steppe zone of Russia for a period from 1950 to 1990 is analyzed. By the end of this period and in the subsequent years, the areas under irrigation reduced considerably, and the soil productivity worsened. This was caused by the improper design of irrigation systems, on the one hand, and by the low tolerance of chernozems toward increased moistening upon irrigation, on the other hand. The analysis of the factors and regimes of soil formation under irrigation conditions shows that irrigation-induced changes in the soil hydrology also lead to changes in the soil physicochemical, biochemical, and other properties. In particular, changes in the composition of exchangeable cations lead to the development of solonetzic process. In many areas, irrigation of chernozems was accompanied by the appearance of solonetzic, vertic, saline, and eroded soils. The development of soil degradation processes is described. In general, the deterioration of irrigated chernozems was related to the absence of adequate experience in irrigation of steppe soils, unskilled personnel, improper regime of irrigation, and excessively high rates of watering. In some cases, the poor quality of irrigation water resulted in the development of soil salinization and alkalization. To improve the situation, the training of personnel is necessary; the strategy of continuous irrigation should be replaced by the strategy of supplementary irrigation in the critical periods of crop development.     

Genotypic differences in the antioxidant and carbon–nitrogen metabolism of acid-tolerant and acid-sensitive rice (Oryzasativa L.) cultivars under acid stress

A pot experiment was conducted to investigate differences in antioxidative defence and carbon–nitrogen metabolism between acid-tolerant (YJSM) and acid-sensitive (YHSM) rice cultivars under acid stress. Acid-tolerant and acid-sensitive rice were planted in both acidic soil (pH 4.21) and normal soil (pH 6.13). Forty-eight days after sowing, rice shoots and roots from four treatments were collected, and the other four replicates were harvested at seed maturity. The results revealed that the grain yield of acid-tolerant YJSM was significantly higher than that of acid-sensitive YHSM under acid stress. The activities of antioxidant enzymes (superoxide dismutase and catalase) and contents of non-enzymatic antioxidants (ascorbate and reduced glutathione) of acid-tolerant YJSM were both higher than those of acid-sensitive YHSM under acid stress. Moreover, the enzyme activities (nitrate reductase, glutamine synthetase, glutamate synthase and glutamate dehydrogenase) and product contents (soluble sugar and soluble protein) of carbon–nitrogen metabolism of acid-tolerant YJSM were higher than those of acid-sensitive YHSM under acid stress. The NO₃^–N and carbon (C) contents in leaves of acid-tolerant YJSM were both significantly higher than those of acid-sensitive YHSM under acid stress. This study suggests that the acid-tolerant rice cultivar has better antioxidative defence and carbon–nitrogen metabolism systems than the acid-sensitive rice cultivar and is more effective in resisting acid stress.     

Review of Trends in Soil Fertility Research (2007–2016) using Scopus Database

A critical analysis of publications on soil fertility was carried out using data from Scopus database for the period of 2007–2016. A total of 16,612 articles were found relating to soil fertility. An exponential increase was evident from the review of published literature and scientists involved in the soil fertility research also increased over period of time. The journals Soil Science and Plant Nutrition and Acta Ecologica Sinica were major publishers of the soil fertility research. Giller K. E. from Wageningen University, The Netherlands was a major contributor followed by Salvati L. of Centro Per Lo Studio Delle Relazioni Piñata-Suolo, Italy. China was the most productive country with 3323 articles. Cluster analysis of author-supplied keywords showed five clusters, namely, desertification, soil organic carbon, plant nutrition, nitrogen, and geostatic. This work will be useful to researchers to know the trends in soil fertility research.     

Mitochondrial genetic diversity and population structuring of UK bottlenose dolphins (Tursiops truncatus): is the NE Scotland population demographically and geographically isolated?

Concern has been expressed over the status of the bottlenose dolphin population that uses the Moray Firth and adjacent waters in NE Scotland. Consequently, part of this population's range has been proposed as a Special Area of Conservation. Efforts to manage and monitor the status of this population require information on the level of genetic diversity within the population and its genetic relatedness to neighbouring populations to appropriately designate units for management and monitoring. Here we examine mitochondrial genetic diversity within the NE Scotland population, and compare this to other regions around the UK and Ireland. Sequence analysis of 549bp of the mitochondrial DNA control region identified eight unique haplotypes in a sample of 29 individuals. Analysis of molecular variance suggests that the Moray Firth population is genetically more closely related to Welsh animals than to its nearest neighbour population in west Scotland. Furthermore, measures of within-population genetic diversity were markedly lower in the Moray Firth than any other sampled region. The low levels of mtDNA genetic variability observed and its apparent geographic isolation provide further support for the precautionary approach currently being applied to the management of this population, despite the lack of direct evidence of harm.     

Genetic diversity and population structure in a regional collection of Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet)

Genetic Resources and Crop Evolution - Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal &amp; Baudet) is an important source of protein and essential nutrients that...